Plotting and visualization tools - Revision history

Andrea Ferretti: /* Avogadro */

2021-03-18T16:39:39Z

Avogadro

← Older revision		Revision as of 16:39, 18 March 2021
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	$> sudo apt-get install avogadro		$> sudo apt-get install avogadro

			If the package is not found (while it should), consider issuing

			$> sudo apt-get update

			and then re-try with the install command.

	[[File:Avogadro.png\|thumb]]		[[File:Avogadro.png\|thumb]]

2021-03-18T10:20:10Z

Avogadro

← Older revision		Revision as of 10:20, 18 March 2021
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	Avogadro is a free open source advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modelling, bioinformatics, materials science, and related areas. It offers flexible high-quality rendering and a powerful plugin architecture.		Avogadro is a free open source advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modelling, bioinformatics, materials science, and related areas. It offers flexible high-quality rendering and a powerful plugin architecture.

	Avogadro it is not installed in the VM, but you can install by typing		Avogadro it is not installed in the VM, but you can install by typing:

	$> sudo apt-get install avogadro		$> sudo apt-get install avogadro

2020-11-25T12:36:19Z

Avogadro

← Older revision		Revision as of 12:36, 25 November 2020
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	[[File:Avogadro.png\|thumb]]		[[File:Avogadro.png\|thumb]]

	With Avogadro you can.		With Avogadro you can:


			* Visualize molecular structurea
			* Build and manipulate molecules
			* Measure distance and bonding
			* Optimize geometries
			* Create animations

	A full guide of the software can be found at the [https://avogadro.cc Avogadro] webpage		A full guide of the software can be found at the [https://avogadro.cc Avogadro] webpage

2020-11-25T12:34:24Z

Avogadro

← Older revision		Revision as of 12:34, 25 November 2020
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	==Avogadro==		==Avogadro==

	Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modelling, bioinformatics, materials science, and related areas. It offers flexible high-quality rendering and a powerful plugin architecture.		Avogadro is a free open source advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modelling, bioinformatics, materials science, and related areas. It offers flexible high-quality rendering and a powerful plugin architecture.

	Avogadro it is not installed in the VM, but you can install by typing		Avogadro it is not installed in the VM, but you can install by typing
Line 111:		Line 111:
	$> sudo apt-get install avogadro		$> sudo apt-get install avogadro

			[[File:Avogadro.png\|thumb]]

	[~~[File~~:Avogadro~~.png\|thumb]~~]		With Avogadro you can.



			A full guide of the software can be found at the [https://avogadro.cc Avogadro] webpage

2020-11-25T12:31:20Z

Avogadro

← Older revision		Revision as of 12:31, 25 November 2020
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	==Avogadro==		==Avogadro==

			Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modelling, bioinformatics, materials science, and related areas. It offers flexible high-quality rendering and a powerful plugin architecture.

			Avogadro it is not installed in the VM, but you can install by typing

			$> sudo apt-get install avogadro


			[[File:Avogadro.png\|thumb]]

2020-11-25T12:28:54Z

← Older revision		Revision as of 12:28, 25 November 2020
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	Documentation can be found at [http://www.xcrysden.org xcrysden] website		Documentation can be found at [http://www.xcrysden.org xcrysden] website


			==Avogadro==

2020-11-25T12:19:08Z

Xcrysden

← Older revision		Revision as of 12:19, 25 November 2020
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	$> xcrysden --pwi ./LAB_1/test_diamond/scf.diamond.in		$> xcrysden --pwi ./LAB_1/test_diamond/scf.diamond.in

	where you can		where you can:

	* Zoom the structure		* Zoom the structure

2020-11-25T12:18:58Z

Xcrysden

← Older revision		Revision as of 12:18, 25 November 2020
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	where you can		where you can

	* Zoom the structure		* Zoom the structure
	* Rotate		* Rotate
	* Translate		* Translate
	* Add units of your crystal		* Add units of your crystal
	* Lighting on/off		* Lighting on/off
	* Print the structure in a file		* Print the structure in a file
	* Comput bond lenghts/angles		* Comput bond lenghts/angles
	* View the Brillouin zone # Tools ->k-path		* View the Brillouin zone # Tools ->k-path
	* View 3D isosurfaces (e.g. densities) #Tools--> Data grid --> Isovalue --> Submit		* View 3D isosurfaces (e.g. densities) #Tools--> Data grid --> Isovalue --> Submit

	Documentation can be found at [http://www.xcrysden.org xcrysden] website		Documentation can be found at [http://www.xcrysden.org xcrysden] website

2020-11-25T12:18:41Z

Xcrysden

← Older revision		Revision as of 12:18, 25 November 2020
Line 90:		Line 90:
	where you can		where you can

	*Zoom the structure		* Zoom the structure
	*Rotate		* Rotate
	*Translate		* Translate
	*Add units of your crystal		* Add units of your crystal
	*Lighting on/off		* Lighting on/off
	*Print the structure in a file		* Print the structure in a file
	*Comput bond lenghts/angles		* Comput bond lenghts/angles
	*View the Brillouin zone # Tools ->k-path		* View the Brillouin zone # Tools ->k-path
	*View 3D isosurfaces (e.g. densities) #Tools--> Data grid --> Isovalue --> Submit		* View 3D isosurfaces (e.g. densities) #Tools--> Data grid --> Isovalue --> Submit

	Documentation can be found at [http://www.xcrysden.org xcrysden] website		Documentation can be found at [http://www.xcrysden.org xcrysden] website

2020-11-25T12:18:26Z

Xcrysden

← Older revision		Revision as of 12:18, 25 November 2020
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	$> xcrysden --help # Short guide		$> xcrysden --help # Short guide
	$> xcrysden --pwi ~~Si-bulk~~.in. #Open a QE input file		$> xcrysden --pwi scf.diamod.in #Open a QE input file
	$> xcrysden --pwo ~~Si-bulk~~.out #Open a QE output file		$> xcrysden --pwo scd.diamond.out #Open a QE output file
	$> xcrysden --xsf charge.xsf #Open a saved xcrysden file		$> xcrysden --xsf charge.xsf #Open a saved xcrysden file
	$> xcrysden --xyz molecule.xyz #Open a Standard “Angstrom” format		$> xcrysden --xyz molecule.xyz #Open a Standard “Angstrom” format

	[[File:Screenshot 2020-11-25 at 13.12.18.png\|thumb]]		[[File:Screenshot 2020-11-25 at 13.12.18.png\|thumb]]

			Here it is an example of

			$> xcrysden --pwi ./LAB_1/test_diamond/scf.diamond.in

			where you can

			*Zoom the structure
			*Rotate
			*Translate
			*Add units of your crystal
			*Lighting on/off
			*Print the structure in a file
			*Comput bond lenghts/angles
			*View the Brillouin zone # Tools ->k-path
			*View 3D isosurfaces (e.g. densities) #Tools--> Data grid --> Isovalue --> Submit

	Documentation can be found at [http://www.xcrysden.org xcrysden] website		Documentation can be found at [http://www.xcrysden.org xcrysden] website